diff --git a/README.md b/README.md index 85c3e5a35a471f86e0a8ace10626b63567d83aef..b55478da9c4cdbe9458b8660a30d0b9a1c3e7f72 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,13 @@ # Topo2 implementation into LAMMPS with external code We model a torsionally relaxed (nicked) DNA plasmid 7.2 kbp-long as a bead-spring polymer made of 1000 beads with bead-size σ=2.5 nm=7.3 bp and connected by finitely extensible springs. The persistence length of the polymer is set to lp = 50 nm. Beads interact via a purely -steric Lennard-Jones repulsion while the TopoII-bound segment is modelled as a 50 beads (L=360 bp)-long segment displaying soft interactions with the other beads thereby allowing the TopoII-bound segment to undergo strand-crossing with a small energy penalty (2 kBT). For details in the model and the system used we refer the reader to our paper: ***D. Michieletto, et al. "Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation"*** +steric Lennard-Jones repulsion while the TopoII-bound segment is modelled as a 50 beads (L=360 bp)-long segment displaying soft interactions with the other beads thereby allowing the TopoII-bound segment to undergo strand-crossing with a small energy penalty (2 kBT). For details in the model and the system used we refer the reader to our paper: ***D. Michieletto, et al. "Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation"***. + +The position of the TopoII-bound segment can be either: + +* Static: +* Random: +* Jump to maximum density: + +